Cell-free DNA in maternal plasma comprises a mixture of fetal and maternal DNA. Noninvasive prenatal measurements of maternal plasma can be used to detect subchromosomal copy number aberrations (CNAs) by counting DNA fragments from subchromosomal regions. But, the counting does not distinguish fetal DNA from maternal DNA. Therefore, aberrations detected by counting DNA fragments could be derived from the fetus or the mother. Thus, when a mother herself is a carrier of a CNA, one could not discern if her fetus has inherited the CNA. In addition, false-positive results would become more prevalent when more subchromosomal regions are analyzed.
Embodiments can address these and other problems.